A comparative analysis of multiple sequence alignments for biological data

被引：3

作者：

Manzoor, Umar ^{[1
]}

Shahid, Sarosh ^{[2
]}

Zafar, Bassam ^{[1
]}

机构：

[1] King Abdulaziz Univ, Fac Comp & Informat Technol, Jeddah 21413, Saudi Arabia

[2] Natl Univ Comp & Emerging Sci, Dept Comp Sci, Islamabad, Pakistan

来源：

BIO-MEDICAL MATERIALS AND ENGINEERING | 2015年 / 26卷

关键词：

Multiple sequence alignment; clustalW; k-align; muscle; mafft; t-coffee; progressive alignment;

D O I：

10.3233/BME-151479

中图分类号：

R318 [生物医学工程];

学科分类号：

0831 ;

摘要：

Multiple sequence alignment plays a key role in the computational analysis of biological data. Different programs are developed to analyze the sequence similarity. This paper highlights the algorithmic techniques of the most popular multiple sequence alignment programs. These programs are then evaluated on the basis of execution time and scalability. The overall performance of these programs is assessed to highlight their strengths and weaknesses with reference to their algorithmic techniques. In terms of overall alignment quality, T-Coffee and Mafft attain the highest average scores, whereas K-align has the minimum computation time.

引用

页码：S1781 / S1789

页数：9

共 50 条

[31] AltAVisT: Comparing alternative multiple sequence alignments
Morgenstern, B
Goel, S
Sczyrba, A
Dress, A
BIOINFORMATICS, 2003, 19 (03) : 425 - 426
[32] CONSEQUENCES : CONstrained SEQUENCE alignmentS With Multiple UserWeights
West, Elizabeth
Daling, Kyle
Miller, Courtney
Rosales, Wes
Vukovic, Sasa
Jagodzinski, Filip
ACM-BCB'19: PROCEEDINGS OF THE 10TH ACM INTERNATIONAL CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND HEALTH INFORMATICS, 2019, : 574 - 579
[33] Sequence Selection for Multiple Alignments of Transmembrane Proteins
Nishio, Takuhiro
Ohta, Teruyuki
Kaneko, Sunao
Shimizu, Toshio
INFORMATION-AN INTERNATIONAL INTERDISCIPLINARY JOURNAL, 2009, 12 (01): : 235 - 242
[34] COFFEE: An objective function for multiple sequence alignments
Notredame, C
Holm, L
Higgins, DG
BIOINFORMATICS, 1998, 14 (05) : 407 - 422
[35] On Using Consistency Consistently in Multiple Sequence Alignments
Joao, Mario, Jr.
Senat, Alexandre C.
Rebello, Vinod E. F.
2022 IEEE 36TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM WORKSHOPS (IPDPSW 2022), 2022, : 152 - 161
[36] Progressive multiple sequence alignments from triplets
Kruspe, Matthias
Stadler, Peter F.
BMC BIOINFORMATICS, 2007, 8 (1)
[37] FAST AND SENSITIVE MULTIPLE SEQUENCE ALIGNMENTS ON A MICROCOMPUTER
HIGGINS, DG
SHARP, PM
COMPUTER APPLICATIONS IN THE BIOSCIENCES, 1989, 5 (02): : 151 - 153
[38] Measuring the distance between multiple sequence alignments
Blackburne, Benjamin P.
Whelan, Simon
BIOINFORMATICS, 2012, 28 (04) : 495 - 502
[39] State of the art: refinement of multiple sequence alignments
Chakrabarti, Saikat
Lanczycki, Christopher J.
Panchenko, Anna R.
Przytycka, Teresa M.
Thiessen, Paul A.
Bryant, Stephen H.
BMC BIOINFORMATICS, 2006, 7 (1)
[40] Identifying subset errors in multiple sequence alignments
Roy, Aparna
Taddese, Bruck
Vohra, Shabana
Thimmaraju, Phani K.
Illingworth, Christopher J. R.
Simpson, Lisa M.
Mukherjee, Keya
Reynolds, Christopher A.
Chintapalli, Sree V.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2014, 32 (03): : 364 - 371

← 1 2 3 4 5 →